Updated pyproject.toml, replaced interp1d to spectres resampling to c…

…onserve flux, allow for negative extinction, extinction support in ReadPlanck, support for grids with log(12CO/13CO) parameter

docs/tutorials/synthetic_photometry.ipynb

@@ -257,7 +257,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next, we use the [SyntheticPhotometry](https://species.readthedocs.io/en/latest/species.phot.html#species.phot.syn_phot.SyntheticPhotometry) class to calculate the flux and magnitude for the [MKO/NSFCam.J](http://svo2.cab.inta-csic.es/svo/theory/fps/index.php?id=MKO/NSFCam.J&&mode=browse&gname=MKO&gname2=NSFCam#filter) filter. We first create and instance of [SyntheticPhotometry](https://species.readthedocs.io/en/latest/species.phot.html#species.phot.syn_phot.SyntheticPhotometry) with the filter name from the SVO website."
+    "Next, we use the [SyntheticPhotometry](https://species.readthedocs.io/en/latest/species.phot.html#species.phot.syn_phot.SyntheticPhotometry) class to calculate the flux and magnitude for the [MKO/NSFCam.J](http://svo2.cab.inta-csic.es/svo/theory/fps/index.php?id=MKO/NSFCam.J&&mode=browse&gname=MKO&gname2=NSFCam#filter) filter. We first create an instance of [SyntheticPhotometry](https://species.readthedocs.io/en/latest/species.phot.html#species.phot.syn_phot.SyntheticPhotometry) with the filter name from the SVO website."
    ]
   },
   {

pyproject.toml

@@ -26,7 +26,16 @@ Repository = "https://github.com/tomasstolker/species"
 Issues = "https://github.com/tomasstolker/species/issues"
 
 [tool.setuptools]
-packages = ["species"]
+packages = [
+    "species",
+    "species.core",
+    "species.data",
+    "species.fit",
+    "species.phot",
+    "species.plot",
+    "species.read",
+    "species.util"
+]
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}

species/data/database.py

@@ -932,7 +932,7 @@ def add_object(
         units : dict, None
             Dictionary with the units of the data provided with
             ``flux_density`` and ``spectrum``. Only required if
-            the wavelength units are not :math:`\\mu\\text{m}^{-1}`
+            the wavelength units are not :math:`\\mu\\text{m}`
             and/or the flux units are not provided as
             :math:`\\text{W} \\text{m}^{-2} \\mu\\text{m}^{-1}`.
             Otherwise, the argument of ``units`` can be set to
@@ -1077,7 +1077,7 @@ def add_object(
                     except KeyError:
                         warnings.warn(
                             f"Filter '{mag_item}' is not available on the SVO Filter "
-                            f"Profile Service so a flux calibration can not be done. "
+                            f"Profile Service so a flux calibration cannot be done. "
                             f"Please add the filter manually with the 'add_filter' "
                             f"function. For now, only the '{mag_item}' magnitude of "
                             f"'{object_name}' is stored."
@@ -1105,7 +1105,7 @@ def add_object(
                         except KeyError:
                             warnings.warn(
                                 f"Filter '{mag_item}' is not available on the SVO "
-                                f"Filter Profile Service so a flux calibration can not "
+                                f"Filter Profile Service so a flux calibration cannot "
                                 f"be done. Please add the filter manually with the "
                                 f"'add_filter' function. For now, only the "
                                 f"'{mag_item}' magnitude of '{object_name}' is "
@@ -1346,7 +1346,7 @@ def add_object(
 
                                 if spec_item not in read_spec:
                                     raise ValueError(
-                                        f"The spectrum data from {spec_value[0]} can not "
+                                        f"The spectrum data from {spec_value[0]} cannot "
                                         f"be read. The data format should be 2D with "
                                         f"3 columns."
                                     )
@@ -1357,14 +1357,14 @@ def add_object(
 
                         except UnicodeDecodeError:
                             raise ValueError(
-                                f"The spectrum data from {spec_value[0]} can not "
+                                f"The spectrum data from {spec_value[0]} cannot "
                                 "be read. Please provide a FITS or ASCII file."
                             )
 
                         if data.ndim != 2 or 3 not in data.shape:
                             raise ValueError(
                                 f"The spectrum data from {spec_value[0]} "
-                                "can not be read. The data format "
+                                "cannot be read. The data format "
                                 "should be 2D with 3 columns."
                             )
 
@@ -1530,7 +1530,7 @@ def add_object(
 
                                 if spec_item not in read_cov:
                                     raise ValueError(
-                                        f"The covariance matrix from {spec_value[1]} can not "
+                                        f"The covariance matrix from {spec_value[1]} cannot "
                                         f"be read. The data format should be 2D with the "
                                         f"same number of wavelength points as the "
                                         f"spectrum."
@@ -1542,14 +1542,14 @@ def add_object(
                         except UnicodeDecodeError:
                             raise ValueError(
                                 f"The covariance matrix from {spec_value[1]} "
-                                f"can not be read. Please provide a "
+                                f"cannot be read. Please provide a "
                                 f"FITS or ASCII file."
                             )
 
                         if data.ndim != 2 or data.shape[0] != data.shape[1]:
                             raise ValueError(
                                 f"The covariance matrix from {spec_value[1]} "
-                                f"can not be read. The data format "
+                                f"cannot be read. The data format "
                                 f"should be 2D with the same number of "
                                 f"wavelength points as the spectrum."
                             )

species/data/model_data/model_data.json

@@ -2,17 +2,17 @@
     "ames-cond": {
         "parameters": ["teff", "logg"],
         "name": "AMES-Cond",
-        "file size": "150 MB",
+        "file size": "57 MB",
         "wavelength range": [0.5, 40],
-        "lambda/d_lambda": 4000,
+        "lambda/d_lambda": 2000,
         "teff range": [100, 6600]
     },
     "ames-dusty": {
         "parameters": ["teff", "logg"],
         "name": "AMES-Dusty",
-        "file size": "58 MB",
+        "file size": "22 MB",
         "wavelength range": [0.5, 40],
-        "lambda/d_lambda": 4000,
+        "lambda/d_lambda": 2000,
         "teff range": [500, 4000]
     },
     "atmo": {
@@ -100,7 +100,7 @@
     "bt-nextgen": {
         "parameters": ["teff", "logg", "feh"],
         "name": "BT-NextGen",
-        "file size": "343 MB",
+        "file size": "328 MB",
         "wavelength range": [0.1, 5000],
         "lambda/d_lambda": 2000,
         "teff range": [2600, 30000]
@@ -140,22 +140,42 @@
         "reference": "Helling et al. (2008)",
         "url": "https://ui.adsabs.harvard.edu/abs/2008ApJ...675L.105H"
     },
-    "exo-rem": {
+    "exo-rem-cloud-r500": {
         "parameters": ["teff", "logg", "feh", "c_o_ratio"],
         "name": "Exo-REM",
-        "file size": "643 MB",
+        "file size": "703 MB",
         "wavelength range": [0.35, 250.0],
         "lambda/d_lambda": 500,
         "teff range": [400, 2000],
         "reference": "Charnay et al. (2018)",
         "url": "https://ui.adsabs.harvard.edu/abs/2018ApJ...854..172C"
     },
-    "exo-rem-highres": {
+    "exo-rem-nocloud-r500": {
         "parameters": ["teff", "logg", "feh", "c_o_ratio"],
         "name": "Exo-REM",
-        "file size": "22 GB",
+        "file size": "508 MB",
+        "wavelength range": [0.35, 250.0],
+        "lambda/d_lambda": 500,
+        "teff range": [400, 2000],
+        "reference": "Charnay et al. (2018)",
+        "url": "https://ui.adsabs.harvard.edu/abs/2018ApJ...854..172C"
+    },
+    "exo-rem-cloud-r20000": {
+        "parameters": ["teff", "logg", "feh", "c_o_ratio"],
+        "name": "Exo-REM",
+        "file size": "21 GB",
         "wavelength range": [0.67, 250.0],
-        "lambda/d_lambda": 20000,
+        "lambda/d_lambda": 500,
+        "teff range": [400, 2000],
+        "reference": "Charnay et al. (2018)",
+        "url": "https://ui.adsabs.harvard.edu/abs/2018ApJ...854..172C"
+    },
+    "exo-rem-cloud-r20000-isotopes": {
+        "parameters": ["teff", "logg", "feh", "c_o_ratio", "log_co_iso"],
+        "name": "Exo-REM",
+        "file size": "239 MB",
+        "wavelength range": [0.67, 250.0],
+        "lambda/d_lambda": 500,
         "teff range": [400, 2000],
         "reference": "Charnay et al. (2018)",
         "url": "https://ui.adsabs.harvard.edu/abs/2018ApJ...854..172C"

species/data/model_data/model_spectra.py

@@ -13,7 +13,7 @@
 import numpy as np
 import pooch
 
-from scipy.interpolate import interp1d
+from spectres.spectral_resampling_numba import spectres_numba
 from typeguard import typechecked
 
 from species.util.core_util import print_section
@@ -245,6 +245,11 @@ def add_model_grid(
     else:
         ad_index = None
 
+    if "log_co_iso" in model_info["parameters"]:
+        log_co_iso = []
+    else:
+        log_co_iso = None
+
     flux = []
 
     print()
@@ -319,6 +324,10 @@ def add_model_grid(
                 param_index = file_split.index("adindex") + 1
                 ad_index.append(float(file_split[param_index]))
 
+            if log_co_iso is not None:
+                param_index = file_split.index("coiso") + 1
+                log_co_iso.append(float(file_split[param_index]))
+
             empty_message = len(print_message) * " "
             print(f"\r{empty_message}", end="")
 
@@ -363,8 +372,14 @@ def add_model_grid(
                     flux.append(data_flux[wavel_select])  # (W m-2 um-1)
 
                 else:
-                    flux_interp = interp1d(data_wavel, data_flux)
-                    flux_resample = flux_interp(wavelength)
+                    flux_resample = spectres_numba(
+                        wavelength,
+                        data_wavel,
+                        data_flux,
+                        spec_errs=None,
+                        fill=np.nan,
+                        verbose=True,
+                    )
 
                     if np.isnan(np.sum(flux_resample)):
                         raise ValueError(
@@ -397,6 +412,9 @@ def add_model_grid(
     if ad_index is not None:
         ad_index = np.asarray(ad_index)
 
+    if log_co_iso is not None:
+        log_co_iso = np.asarray(log_co_iso)
+
     data_sorted = sort_data(
         np.asarray(teff),
         logg,
@@ -405,6 +423,7 @@ def add_model_grid(
         fsed,
         log_kzz,
         ad_index,
+        log_co_iso,
         wavelength,
         np.asarray(flux),
     )

species/fit/compare_spectra.py

@@ -407,7 +407,7 @@ def compare_model(
         fix_logg : float, None
             Fix the value of :math:`\\log(g)`, for example if estimated
             from gravity-sensitive spectral features. Typically,
-            :math:`\\log(g)` can not be accurately determined when
+            :math:`\\log(g)` cannot be accurately determined when
             comparing the spectra over a broad wavelength range.
         scale_spec : list(str), None
             List with names of observed spectra to which an additional

species/fit/fit_model.py

@@ -1469,13 +1469,13 @@ def _lnlike_func(
                         warnings.warn(
                             "The 'logg' parameter is not used "
                             f"by the '{self.model}' model so "
-                            "the mass prior can not be applied."
+                            "the mass prior cannot be applied."
                         )
 
                     elif "radius" not in self.modelpar:
                         warnings.warn(
                             "The 'radius' parameter is not fitted "
-                            "so the mass prior can not be applied."
+                            "so the mass prior cannot be applied."
                         )
 
             elif prior_key[:6] == "ratio_":
@@ -2506,7 +2506,7 @@ def _lnlike_ultranest(params: np.ndarray) -> Union[float, np.float64]:
             ln_like = self._lnlike_func(params)
 
             if not np.isfinite(ln_like):
-                # UltraNest can not handle np.inf in the likelihood
+                # UltraNest cannot handle np.inf in the likelihood
                 ln_like = -1e100
 
             return ln_like

species/fit/retrieval.py

@@ -3573,7 +3573,7 @@ def setup_retrieval(
 
         elif "fsed_1" in bounds or "fsed_2" in bounds:
             raise ValueError(
-                "The cross_corr parameter can not be "
+                "The cross_corr parameter cannot be "
                 "used with multiple fsed parameters."
             )
 
@@ -3663,7 +3663,7 @@ def setup_retrieval(
                 if param_item in bounds:
                     warnings.warn(
                         f"The '{param_item}' parameter "
-                        "can not be used if the "
+                        "cannot be used if the "
                         "'abund_nodes' argument is set. "
                         "The  prior boundaries of "
                         f"'{param_item}' will therefore "

species/phot/syn_phot.py

@@ -357,7 +357,7 @@ def spectrum_to_flux(
             error_flux = np.std(phot_random)
 
         elif error is not None and np.any(np.isnan(error)):
-            warnings.warn("Spectum contains NaN so can not calculate the error.")
+            warnings.warn("Spectum contains NaN so cannot calculate the error.")
             error_flux = None
 
         else:
@@ -479,7 +479,7 @@ def spectrum_to_magnitude(
             error_app_mag = np.std(mag_random)
 
         elif error is not None and np.any(np.isnan(error)):
-            warnings.warn("Spectum contains NaN so can not calculate the error.")
+            warnings.warn("Spectum contains NaN so cannot calculate the error.")
             error_app_mag = None
 
         else:

species/plot/plot_spectrum.py

@@ -1244,7 +1244,7 @@ def plot_spectrum(
 
         if obj_index is None:
             raise ValueError(
-                "ObjectBox not found so can not create "
+                "ObjectBox not found so cannot create "
                 "residuals. Please add an ObjectBox to "
                 "the list of boxes."
             )